PYQ – MZO-004: Systematics, Biodiversity and Evolution (Solved Q&A) | MZO-004 | MSCZOO | M.Sc.Zoology | IGNOU | December 2024
M.Sc. (Zoology) (MSCZOO)
Term-End Examination
December, 2024
MZO-004 : SYSTEMATICS, BIODIVERSITY AND EVOLUTION
Time : 2 Hours| Maximum Marks : 50
Note: (i) Attempt any five questions.
(ii) All questions carry equal marks.
1. Explain the fundamental principles of evolution that are the foundations of modern evolutionary biology. (10 Marks)
Modern evolutionary biology is based on certain basic principles that explain how populations change over time and how new species originate. These principles help us understand the mechanisms behind evolutionary processes. Though evolution can involve many complex interactions, there are five main principles that form the foundation of this field:
1. Genetic Variation
Genetic variation is the raw material for evolution. It means the differences in DNA among individuals of a population. These differences arise due to mutation, recombination during meiosis and sometimes gene flow from other populations. Without variation, evolution cannot occur because there will be no differences for natural selection to act upon. Variations can be in physical traits, metabolic pathways, or even behaviour, and these may influence survival and reproduction.
2. Natural Selection
This principle was first explained by Charles Darwin. Natural selection is a non-random process in which organisms with traits that provide better survival or reproduction in a particular environment tend to leave more offspring. Over generations, these traits become more common. For example, in a cold environment, animals with thicker fur may survive better. Natural selection works only if heritable variation is present.
3. Genetic Drift
Unlike natural selection, genetic drift is a random process. It affects smaller populations more strongly. Certain alleles can become more or less frequent in a population by chance events like natural disasters. Over time, this can lead to loss of genetic diversity and fixation of neutral or even slightly harmful alleles. One example is the founder effect where a new population starts from a small group, carrying only a small part of the original genetic variation.
4. Gene Flow
Gene flow is the movement of alleles between populations when individuals migrate and breed. It introduces new genetic material into a population and increases genetic diversity. It also reduces differences between populations. If two populations of the same species keep exchanging genes, they are less likely to become separate species.
Speciation and Common Descent
Speciation occurs when populations become isolated due to barriers like geography or behaviour and evolve independently. With time, genetic differences become so great that individuals from different populations cannot interbreed. This leads to formation of new species. Common descent means all organisms share a common ancestor. Evidence for this includes similarities in DNA sequences, embryonic development and fossil records.
2. Describe the theory of spontaneous generation. Discuss the Urey-Miller experiment and its conclusion. (10 Marks)
The theory of spontaneous generation, also known as abiogenesis, was an old scientific belief which stated that life could arise suddenly and directly from non-living matter. This idea was widely accepted until the 17th century. According to this theory, organisms like maggots, frogs, or even mice could appear from decaying meat, mud, or other lifeless substances. Many scientists of that time supported this theory through different observations and experiments. For example, in the 17th century, Van Helmont claimed that mice could be produced by placing wheat and dirty clothes in a closed container for a few weeks. Similarly another scientist, John Needham, tried to support this idea by boiling meat broth and sealing it. Later, he observed microbial growth and concluded that life had appeared spontaneously. However, this theory was later disproved by experiments from scientists like Francesco Redi in 1668 through the Meat Experiment, Lazzaro Spallanzani in 1768 through the Boiled Broth Experiment, and Louis Pasteur in 1861 using the Swan Neck Flask Experiment who showed that life comes from pre-existing life.
Even though spontaneous generation in the classical sense was disproved, a modified form of abiogenesis continued to exist in origin-of-life studies. Scientists proposed that while modern organisms arise from other organisms, the first life on Earth must have come from non-living chemical compounds under early Earth conditions. This led to the famous Miller-Urey experiment, which tested the chemical basis of the origin of life.
The Miller-Urey experiment, conducted in 1953 by Stanley Miller under the guidance of Harold Urey, was designed to simulate the conditions of early Earth's atmosphere and oceans. They hypothesized that the primitive atmosphere contained gases like methane (CH₄), ammonia (NH₃), hydrogen (H₂) and water vapor (H₂O), and that energy from lightning or UV radiation triggered chemical reactions to form organic molecules.
In the experiment, Miller used a closed glass apparatus containing these gases and a reservoir of boiling water to mimic the early ocean. Electrical sparks were passed through the gas mixture to simulate lightning. After running the experiment for a week, they analyzed the liquid in the apparatus and found that several organic compounds had formed, including amino acids like glycine and alanine, which are the building blocks of proteins.
The conclusion of the Miller-Urey experiment was that under the presumed conditions of early Earth, simple organic molecules essential for life could be synthesized from inorganic compounds in the presence of energy. This experiment gave strong support to the chemical origin of life theory and showed that life's building blocks could form naturally on a lifeless Earth. It did not produce life itself, but it opened the way for further studies on prebiotic chemistry and the possible pathways through which life could have emerged.
3. (a) What is a phylogenetic tree? Explain the key points about the phylogenetic tree with suitable examples. (5 Marks)
A phylogenetic tree is a diagram that shows the evolutionary relationships among different organisms based on genetic, morphological, or molecular data. It helps to trace the lineage of species from common ancestors and understand their evolutionary history. The structure of a phylogenetic tree includes several important parts. The root represents the most ancient common ancestor of all species in the tree. From the root, branches emerge that show the evolutionary path over time. At the point where a branch splits, a node is formed. Each node represents a common ancestor that gave rise to two or more descendant lineages. The leaves or tips of the branches represent existing species or taxa.
Phylogenetic trees are mainly of two types: rooted and unrooted. A rooted tree shows the direction of evolution from a common ancestor, while an unrooted tree only shows the relationships among organisms without indicating evolutionary paths. These trees are widely used in systematics, taxonomy and comparative genomics.
Key Points About the Phylogenetic Tree
A phylogenetic tree is a diagram that shows evolutionary relationships among different organisms. It is based on shared characteristics and genetic information. These trees help scientists understand how species are related through evolution.
Shows Common Ancestry
- Each branch point or node in the phylogenetic tree represents a common ancestor. Organisms that are connected to the same node share a recent common ancestor.
Direction of Evolution
- The tree usually starts from a single point (the root), which represents the most ancient ancestor. From there, branches extend outward showing the direction of evolutionary changes over time.
Branch Length Can Indicate Time or Change
- In some phylogenetic trees, the length of branches indicates either the amount of evolutionary change or time since divergence.
Based on Morphology or Molecular Data
- Phylogenetic trees can be constructed using morphological features (like body structure) or molecular data (like DNA or protein sequences). Molecular data gives more accurate and detailed results.
Monophyletic, Paraphyletic and Polyphyletic Groups
- A monophyletic group includes an ancestor and all its descendants.
- A paraphyletic group includes the ancestor but not all descendants.
- A polyphyletic group includes organisms from different ancestors.
Helps in Classification and Taxonomy
- It helps in placing organisms into groups (taxa) based on their evolutionary history, not just similarity in appearance.
Example
A simple example is a phylogenetic tree of vertebrates showing relationships among fishes, amphibians, reptiles, birds and mammals. The tree shows that birds and reptiles share a more recent common ancestor than birds and mammals, indicating that birds evolved from reptile-like ancestors.
(b) How will you construct phylogenetic tree by using 16S rRNA gene sequence? (5 Marks)
Phylogenetic trees show the evolutionary relationship among organisms. The 16S rRNA gene is commonly used in prokaryotic taxonomy because it is present in all bacteria and changes very slowly over time. It contains conserved regions for alignment and variable regions for distinguishing species. The following steps explain how to construct a phylogenetic tree using the 16S rRNA gene sequence.
Step 1: DNA Extraction and PCR Amplification
First, genomic DNA is extracted from the organism. The 16S rRNA gene is then amplified using specific primers through Polymerase Chain Reaction (PCR). This ensures that enough copies of the target gene are available for sequencing.
Step 2: Sequencing of 16S rRNA
The amplified gene is sequenced using methods like Sanger sequencing or high-throughput sequencing. The obtained sequence is cleaned and checked for quality.
Step 3: Sequence Alignment
The 16S rRNA sequence is aligned with sequences from known organisms using tools like ClustalW or MUSCLE. Multiple sequence alignment helps to identify conserved and variable regions among different organisms.
Step 4: Phylogenetic Tree Construction
A phylogenetic tree is built using computational tools like MEGA, PhyML, or RAxML. Different methods such as Neighbor-Joining, Maximum Likelihood, or Bayesian Inference are used to predict evolutionary relationships.
Step 5: Interpretation
The resulting tree shows how closely related the organisms are. Branch lengths indicate genetic distance and nodes represent common ancestors.
4. What is molecular clock ? Explain its calibration with suitable examples. (10 Marks)
The molecular clock is a method used in molecular evolution to estimate the time of divergence between species or lineages by analyzing the rate of mutations in DNA or protein sequences. It is based on the idea that genetic mutations accumulate at a relatively constant rate over time in certain parts of the genome, especially in neutral or nearly neutral regions. This idea was first introduced by Emile Zuckerkandl and Linus Pauling in 1962. By comparing genetic differences between two species, scientists can estimate how long ago they shared a common ancestor.
Molecular clocks are widely applied in phylogenetics, evolutionary biology and systematics, especially when fossil records are limited or missing. It has been used in mitochondrial DNA, ribosomal RNA genes and conserved protein sequences like cytochrome c.
Calibration of Molecular Clock
Calibration means adjusting the mutation rate using some known information, so that we can calculate actual divergence time. This process usually follows the steps below:
1. Select a gene or DNA region that is present in all species being compared. This gene must show enough variation over time, like mitochondrial DNA or ribosomal RNA.
2. Collect the genetic sequences of that gene from different organisms.
3. Build a phylogenetic tree using sequence similarity. This tree will show the relationship but not the exact time of divergence yet.
4. Use a calibration point where the actual divergence time is already known. This is done mainly in two ways:
- Fossil Calibration:
- A well-dated fossil is used. For example, if fossil evidence shows that mammals and birds diverged 310 million years ago, that point is fixed on the tree. The number of mutations since that time helps to calculate the mutation rate.
- Geological or Biogeographical Calibration:
- If a major geological event like the splitting of continents is known, it can be used. For example, if two species are found on Africa and South America and the continents split 100 million years ago, that event is used to calibrate divergence.
Once this mutation rate is calibrated, it can be applied to other unknown nodes of the tree to calculate when those divergences happened.
Examples of Molecular Clock
- In human and chimpanzee evolution, mitochondrial DNA has been used with fossil calibration and it estimated divergence around 6 million years ago.
- In bird and mammal studies, cytochrome c gene sequences were compared and fossil data helped calibrate their divergence time to about 310 million years.
- In plant phylogeny, fossil angiosperms were used to calibrate molecular clocks based on chloroplast genes.
5. Write short notes on the following:
(a) Evolution of eukaryotic genome (5 Marks)
The evolution of the eukaryotic genome is marked by major changes that made it larger and more complex than prokaryotic genomes. One of the most important theories explaining this change is the Endosymbiotic Theory, which was first clearly proposed by Lynn Margulis in 1967. According to this theory, organelles like mitochondria and chloroplasts originated from free-living prokaryotes that entered into a symbiotic relationship with early eukaryotic ancestors. These organelles still carry their own circular DNA, which supports the theory.
Another important event in eukaryotic genome evolution is gene duplication. This process created extra copies of genes which later evolved new functions, allowing specialization and complexity in multicellular organisms. Susumu Ohno in 1970 emphasized the importance of gene duplication in evolutionary biology.
Horizontal gene transfer (HGT), especially during early eukaryotic evolution, also contributed new genes from engulfed prokaryotes. Over time, many of these foreign genes became part of the nuclear genome.
Eukaryotic genomes also developed introns and alternative splicing, increasing the protein-coding potential without needing more genes. Moreover, the presence of non-coding DNA, including transposable elements and regulatory sequences, helped in genome regulation and organization.
These events together shaped the highly structured and regulated genome seen in modern eukaryotes.
(b) Secondary and tertiary endosymbiosis (5 Marks)
Endosymbiosis is a natural process in which one living cell lives inside another and both benefit from this relationship. In the history of eukaryotic evolution, this process has helped in the development of complex cell structures like plastids. When such events happen in multiple steps involving eukaryotic cells, they are called secondary and tertiary endosymbiosis.
Secondary Endosymbiosis
Secondary endosymbiosis is a type of symbiotic event where a eukaryotic cell engulfs another eukaryotic cell that already contains a primary plastid. The primary plastid is usually derived from a cyanobacterium through primary endosymbiosis. In secondary endosymbiosis, the engulfed eukaryotic cell is typically a red or green alga. This leads to plastids that have three or four membranes, instead of the usual two seen in primary plastids. The extra membranes are the result of engulfing an entire eukaryotic cell, including its cell membrane and nuclear envelope. Organisms like Euglenids (which took in green algae) and Chromalveolates such as diatoms and brown algae (which took in red algae) are examples of lineages with secondary plastids.
Tertiary Endosymbiosis
Tertiary endosymbiosis is an even more advanced step where a eukaryotic cell engulfs another eukaryote that already has a plastid from secondary endosymbiosis. This results in plastids with even more complex structures and sometimes the plastid may retain parts of the engulfed cell's nucleus or organelles. Tertiary endosymbiosis is seen in some dinoflagellates that replaced their old plastids by engulfing other photosynthetic eukaryotes like haptophytes. These plastids can have unique gene sequences and membrane structures that reflect their complicated evolutionary history.
6. Describe the molecular and genetic basis of speciation. (10 Marks)
Speciation means the formation of new species from already existing ones. This process happens mainly because of genetic changes that slowly build up in isolated populations. These changes stop different groups from mating with each other successfully. At the molecular and genetic level, there are several important factors that cause this reproductive isolation and help in speciation.
1. Mutation and Genetic Variation
The basic source of all genetic change is mutation. Mutations are random changes in the DNA, such as point mutations, insertions, deletions and duplications. These mutations create new alleles in a population. Over time, different populations collect different mutations. If these mutations affect traits like mating behavior or reproductive systems, they can lead to speciation.
2. Genetic Drift and Isolation
In small populations, genetic drift becomes very important. It causes random changes in allele frequency, especially when a population gets separated from the main group. If gene flow is blocked and genetic drift continues, the isolated population becomes genetically different and may form a new species.
3. Natural Selection and Local Adaptation
When different populations live in different environments, natural selection favors different traits. For example, one population may develop traits to survive in dry areas while the other survives in wet areas. These adaptations lead to changes in the gene pool and slowly build reproductive barriers.
4. Chromosomal Rearrangements
Sometimes large changes happen in chromosomes like inversions, translocations, or fusions. These rearrangements may not affect the individual, but when they mate with another individual with a different chromosome structure, the offspring may be sterile or weak. This kind of postzygotic isolation helps in speciation.
5. Regulatory Changes in Gene Expression
Genes are not only controlled by their coding regions but also by regulatory elements like promoters and enhancers. Changes in these regions can lead to different patterns of gene expression. These differences can affect traits like body shape, color, or mating signals, leading to reproductive isolation.
6. Dobzhansky–Muller Incompatibility
When two populations evolve separately, they may develop different genetic changes. Sometimes, when individuals from these populations mate, the combination of their genes may not work properly together. This results in hybrid sterility or inviability. This idea is called Dobzhansky–Muller genetic incompatibility and is a strong force in speciation.
7. Describe the following:
(a) Recent trends in human evolution (5 Marks)
Even though modern humans (Homo sapiens) evolved around 3 lakh years ago, human evolution is still going on. These changes are not very big or sudden, but they are slowly happening at the level of genes, body structure and behavior.
One of the major recent trends is genetic adaptation to environment. For example, in some human populations, adults can digest milk because of a gene for lactose tolerance. This change happened after people started domesticating animals and drinking milk regularly. Another example is seen in Tibetan people, who live at high altitudes. They have changes in the EPAS1 gene that help them survive with less oxygen.
There are also physical changes like smaller jaws and teeth. This is probably because of cooking and eating soft food, which reduced the need for strong chewing muscles. Along with this, the brain has become more complex and specialized for thinking, planning and communication.
Recent DNA research also shows gene mixing between humans and other ancient species like Neanderthals and Denisovans. This mixing helped early humans gain useful traits like better immunity.
Today, modern medicine and lifestyle are also affecting evolution. People with genetic diseases can now live longer because of treatment. So natural selection is working in different ways now compared to the past.
(b) Consequences of horizontal gene transfer in bacteria (5 Marks)
Horizontal gene transfer is a natural process in which bacteria obtain genes from other bacteria or their surroundings without reproduction. Sometimes it happens directly from the environment and sometimes it needs agents like viruses or contact structures. This process helps bacteria change fast and survive in different and difficult conditions.
There are the following major consequences of horizontal gene transfer in bacteria:
1. Spread of Antibiotic Resistance
HGT allows fast sharing of antibiotic resistance genes. If one bacterium develops resistance, it can pass that gene to others, making many bacteria resistant to the same medicine.
2. Increase in Virulence
Some bacteria become more harmful after receiving genes for toxins or other disease-causing features. This increases their ability to cause serious infections.
3. Greater Genetic Diversity
By collecting genes from many sources, bacteria become more adaptable. This helps them survive in difficult conditions like presence of antibiotics or high temperature.
4. Evolution of New Strains
When the new genes get mixed with the main DNA, it can lead to new traits and even formation of new bacterial strains or species.
5. Difficulty in Classification
Because genes are shared across species, it becomes difficult to define clear boundaries between bacterial species. This makes their classification more difficult.
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